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Santhosh KH, Krishna V, Kemparaju K, Manjunatha H, Shashi Kumar R, Mukherjee A, Gomez Mejiba SE, Ramirez DC, Ravindranath BS. β-keto amyrin isolated from Cryptostegia grandiflora R. br. inhibits inflammation caused by Daboia russellii viper venom: Direct binding of β-keto amyrin to phospholipase A 2. Toxicon 2024; 241:107679. [PMID: 38447765 PMCID: PMC11194115 DOI: 10.1016/j.toxicon.2024.107679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/27/2024] [Accepted: 03/03/2024] [Indexed: 03/08/2024]
Abstract
The search for mechanism-based anti-inflammatory therapies is of fundamental importance to avoid undesired off-target effects. Phospholipase A2 (PLA2) activity is a potential molecular target for anti-inflammatory drugs because it fuels arachidonic acid needed to synthesize inflammation mediators, such as prostaglandins. Herein, we aim to investigate the molecular mechanism by which β-keto amyrin isolated from a methanolic extract of Cryptostegia grandiflora R. Br. Leaves can inhibit inflammation caused by Daboia russellii viper (DR) venom that mainly contains PLA2. We found that β-keto amyrin neutralizes DR venom-induced paw-edema in a mouse model. Molecular docking of PLA2 with β-keto amyrin complex resulted in a higher binding energy score of -8.86 kcal/mol and an inhibition constant of 611.7 nM. Diclofenac had a binding energy of -7.04 kcal/mol and an IC50 value of 620 nM, which predicts a poorer binding interaction than β-keto amyrin. The higher conformational stability of β-keto amyrin interaction compared to diclofenac is confirmed by molecular dynamics simulation. β-keto amyrin isolated from C. grandiflora inhibits the PLA2 activity contained in Daboia russellii viper venom. The anti-inflammatory property of β-keto amyrin is due to its direct binding into the active site of PLA2, thus inhibiting its enzyme activity.
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Affiliation(s)
- K H Santhosh
- Department of Biotechnology and Bioinformatics, Kuvempu University, Jnana Sahyadri, Shankaraghatta-577451, Karnataka, India
| | - V Krishna
- Department of Biotechnology and Bioinformatics, Kuvempu University, Jnana Sahyadri, Shankaraghatta-577451, Karnataka, India
| | - K Kemparaju
- Department of Biochemistry, University of Mysore, Manasa Gangotri Campus, Mysore-57006, Karnataka, India
| | - H Manjunatha
- Department of Biochemistry, Jnana Bharathi Campus, Bangalore University, Bangalore- 56005, Karnataka, India
| | - R Shashi Kumar
- Department of Biotechnology and Bioinformatics, Kuvempu University, Jnana Sahyadri, Shankaraghatta-577451, Karnataka, India
| | - A Mukherjee
- Department of Biotechnology, Manipal Institute of Technology, Manipal, Manipal Academy of Higher Education, Manipal- 576104, Karnataka, India
| | - S E Gomez Mejiba
- Laboratory of Nutrition and Experimental Therapeutics, CCT-San Luis-National University of San Luis, San Luis, 5700-San Luis, Argentina.
| | - D C Ramirez
- Laboratory of Experimental and Translational Medicine. CCT-San Luis-National University of San Luis, San Luis, 5700-San Luis, Argentina.
| | - B S Ravindranath
- Department of Biotechnology, Manipal Institute of Technology, Manipal, Manipal Academy of Higher Education, Manipal- 576104, Karnataka, India.
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Kashyap D, Koirala S, Roy R, Saini V, Varshney N, Bagde PH, Samanta S, Kar P, Jha HC. Computational insights into VacA toxin inhibition: harnessing FDA-approved antibiotics against Helicobacter pylori. J Biomol Struct Dyn 2023:1-13. [PMID: 37937550 DOI: 10.1080/07391102.2023.2278080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023]
Abstract
Cancer is a condition in which a few of the body's cells grow beyond its control and spread to other outward regions. Globally, gastric cancer (GC) is third most common cause of cancer-related mortality and the fourth most common kind of cancer. Persistent infection of VacA-positive Helicobacter pylori (H. pylori) modulates cellular physiology and leads to GC. About ∼70% of H. pylori are positive for vacuolating cytotoxin-A (VacA), and it infects ∼80-90% of world populations. Herein, for first time, we repurposed FDA-approved gram-negative antibiotics, which are feasible alternatives to existing regimens and may be used in combinatorial treatment against VacA-positive H. pylori. Out of 110 FDA-approved antibiotics, we retrieved 92 structures, which were screened against the VacA protein. Moreover, we determined that the top eight hit antibiotics viz; cefpiramide, cefiderocol, eravacycline, doxycycline, ceftriaxone, enoxacin, tedizolid, and cefamandole show binding free energies of -9.1, -8.9, -8.1, -8.0, -7.9, -7.8, -7.8 and -7.8 Kcal/mol, respectively, with VacA protein. Finally, we performed 100 ns duplicate MD simulations on the top eight selected antibiotics showing strong VacA binding. Subsequently, five antibiotics, including cefiderocol, cefpiramide, doxycycline, enoxacin, and tedizolid show stable ligand protein distance and good binding affinity revealed by the MM-PBSA scheme. Among the five antibiotics cefiderocol act as the most potent inhibitor (-28.33 kcal/mol). Furthermore, we also identified the hotspot residue like Asn-506, Tyr-529, and Phe-483 which control the interaction. Concisely, we identified antibiotics that can be repurposed against VacA of H. pylori and explored their molecular mechanism of interaction with VacA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dharmendra Kashyap
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Suman Koirala
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Rajarshi Roy
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Vaishali Saini
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Nidhi Varshney
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Pranit Hemant Bagde
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Sunanda Samanta
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
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Koirala S, Roy R, Samanta S, Mahapatra S, Kar P. Plant derived active compounds of ayurvedic neurological formulation, Saraswatharishta as a potential dual leucine zipper kinase inhibitor: an in-silico study. J Biomol Struct Dyn 2023:1-14. [PMID: 37771163 DOI: 10.1080/07391102.2023.2260892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/14/2023] [Indexed: 09/30/2023]
Abstract
Recent findings have highlighted the essential role of dual leucine zipper kinase (DLK) in neuronal degeneration. Saraswatharishta (SWRT), an ayurvedic formulation utilized in traditional Indian medicine, has demonstrated effectiveness in addressing neurodegenerative diseases. Herein, we aim to delve into the atomistic details of the mode of action of phytochemicals present in SWRT against DLK. Our screening process encompassed over 500 distinct phytochemicals derived from the main ingredients of the SWRT formulation. Through a comparative analysis of docking scores and relative poses, we successfully identified four novel compounds, which underwent further investigation via 2 × 500 ns long molecular dynamics (MD) simulations. Among the top four compounds, CID16066851 sourced from the Acorus calamus displayed the most stable complex with DLK. The molecular mechanics Poisson - Boltzmann surface area (MM-PBSA) calculations highlighted the significance of electrostatic and van der Waals interactions in the binding recognition process. Additionally, we identified key residues, namely Phe192, Leu243, Val139, and Leu141, as hotspots that predominantly govern the DLK-inhibitor interaction. Notably, the leading compounds are sourced from the Acorus calamus, Syzygium aromaticum, Zingiber officinale, and Anethum sowa plants present in the SWRT formulation. Overall, the findings of our study hold promise for future drug development endeavors combating neurodegenerative conditions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Suman Koirala
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, MP, India
| | - Rajarshi Roy
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Sunanda Samanta
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, MP, India
| | - Subhasmita Mahapatra
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, MP, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, MP, India
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Das T, Mukhopadhyay C. Molecular dynamics simulations suggest Thiosemicarbazones can bind p53 cancer mutant R175H. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140903. [PMID: 36731759 DOI: 10.1016/j.bbapap.2023.140903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023]
Abstract
Cancer pathologies are associated with the unfolding and aggregation of most recurring mutations in the DNA Binding Domain (DBD) of p53 that coordinate the destabilization of protein. Substitution at the 175th codon with arginine to histidine (R175H, a mutation of large to small side-chain amino acid) destabilizes the DBD by 3 kcal/mol and triggers breasts, lung cancer, etc. Stabilizing the p53 mutant by small molecules offers an attractive drug-targeted anti-cancer therapy. The thiosemicarbazone (TSC) molecules NPC and DPT are known to act as zinc-metallochaperones to reactivate p53R175H. Here, a combination of LESMD simulations for 10 TSC conformations with a p53R175H receptor, single ligand-protein conformation MD, and ensemble docking with multiple p53R175H conformations observed during simulations is suggested to identify the potential binding site of the target protein in light of their importance for the direct TSC - p53R175H binding. NPC binds mutant R175H in the loop region L2-L3, forming pivotal hydrogen bonds with HIS175, pi‑sulfur bonds with TYR163, and pi-alkyl linkages with ARG174 and PRO190, all of which are contiguous to the zinc-binding native site on p53DBD. DPT, on the other hand, was primarily targeting alternative binding sites such as the loop-helix L1/H2 region and the S8 strand. The similar structural characteristics of TSC-bound p53R175H complexes with wild-type p53DBD are thought to be attributable to involved interactions that favour binding free energy contributions of TSC ligands. Our findings may be useful in the identification of novel pockets with druggable properties.
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Affiliation(s)
- Tanushree Das
- Department of Chemistry, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| | - Chaitali Mukhopadhyay
- Department of Chemistry, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India.
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Funk JL, Wertheim BC, Frye JB, Blew RM, Nicholas JS, Chen Z, Bea JW. Association of ß-glucuronidase activity with menopausal status, ethnicity, adiposity, and inflammation in women. Menopause 2023; 30:186-192. [PMID: 36696643 PMCID: PMC9886315 DOI: 10.1097/gme.0000000000002106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
OBJECTIVES Many dietary polyphenols with potential health-promoting benefits undergo hepatic conjugation and circulate as inactive glucuronides that can be cleaved by ß-glucuronidase to reform the bioactive aglycone. Although indirect evidence suggests estrogen may induce ß-glucuronidase, little is known about ß-glucuronidase regulation across women's reproductive lifespan. Correlates of serum ß-glucuronidase activity in healthy premenopausal versus postmenopausal women were therefore examined. METHODS ß-Glucuronidase activity and C-reactive protein (CRP) were assayed in stored serum from the Women's Breast and Bone Density Study, and dual-energy x-ray absorptiometry and anthropometry assessed body composition. Participants were premenopausal (n = 133) or postmenopausal (n = 89), and Hispanic (37%) or non-Hispanic White (63%). Multivariate linear regression models tested associations between ß-glucuronidase and menopausal status, ethnicity, CRP, and body composition metrics, overall and stratified by menopausal status. RESULTS Postmenopausal (vs premenopausal) women were older (60.4 ± 3.7 vs 44.8 ± 2.4 y) with a lower Hispanic ethnicity prevalence (27% vs 44%), and higher serum ß-glucuronidase activity (1.5 ± 0.8 vs 1.3 ± 0.5 U/L) and CRP (4.2 ± 4.4 vs 3.3 ± 4.7 mg/L). Adjusting for confounders, ß-glucuronidase was positively associated with Hispanic ethnicity, CRP, body mass index, and total fat mass (all, P < 0.01), but not menopausal status nor lean mass. Central adiposity measures were also positively associated with ß-glucuronidase with the same covariates. CONCLUSIONS ß-Glucuronidase enzyme activity, upon which polyphenol health-related benefits may depend, is not associated with menopausal status. Future studies are required to determine clinical significance and mechanisms driving ß-glucuronidase associations with ethnicity, inflammation, and adiposity in women.
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Affiliation(s)
- Janet L Funk
- Department of Medicine, College of Medicine, UA
- School of Nutritional Sciences & Wellness, College of Agriculture and Life Science, UA
| | | | | | - Robert M Blew
- School of Nutritional Sciences & Wellness, College of Agriculture and Life Science, UA
- Department of Health Promotion Sciences, Mel and Enid Zuckerman College of Public Health, UA
| | - Jennifer Skye Nicholas
- Department of Epidemiology and Biostatistics Department, Mel and Enid Zuckerman College of Public Health, UA
| | - Zhao Chen
- Department of Epidemiology and Biostatistics Department, Mel and Enid Zuckerman College of Public Health, UA
| | - Jennifer W Bea
- Department of Medicine, College of Medicine, UA
- University of Arizona Cancer Center, UA
- Department of Health Promotion Sciences, Mel and Enid Zuckerman College of Public Health, UA
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Fachel FNS, Frâncio L, Poletto É, Schuh RS, Teixeira HF, Giugliani R, Baldo G, Matte U. Gene editing strategies to treat lysosomal disorders: The example of mucopolysaccharidoses. Adv Drug Deliv Rev 2022; 191:114616. [PMID: 36356930 DOI: 10.1016/j.addr.2022.114616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 09/20/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
Abstract
Lysosomal storage disorders are a group of progressive multisystemic hereditary diseases with a combined incidence of 1:4,800. Here we review the clinical and molecular characteristics of these diseases, with a special focus on Mucopolysaccharidoses, caused primarily by the lysosomal storage of glycosaminoglycans. Different gene editing techniques can be used to ameliorate their symptoms, using both viral and nonviral delivery methods. Whereas these are still being tested in animal models, early results of phase I/II clinical trials of gene therapy show how this technology may impact the future treatment of these diseases. Hurdles related to specific hard-to-reach organs, such as the central nervous system, heart, joints, and the eye must be tackled. Finally, the regulatory framework necessary to advance into clinical practice is also discussed.
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Affiliation(s)
- Flávia Nathiely Silveira Fachel
- Laboratório de Células, Tecidos e Genes - Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, UFRGS, Porto Alegre, RS, Brazil
| | - Lariane Frâncio
- Laboratório de Células, Tecidos e Genes - Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, UFRGS, Porto Alegre, RS, Brazil
| | - Édina Poletto
- Laboratório de Células, Tecidos e Genes - Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Roselena Silvestri Schuh
- Laboratório de Células, Tecidos e Genes - Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, UFRGS, Porto Alegre, RS, Brazil
| | - Helder Ferreira Teixeira
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, UFRGS, Porto Alegre, RS, Brazil
| | - Roberto Giugliani
- Programa de Pós-Graduação em Genética e Biologia Molecular, UFRGS, Porto Alegre, RS, Brazil; Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil; Departamento de Genética, UFRGS, Porto Alegre, RS, Brazil
| | - Guilherme Baldo
- Laboratório de Células, Tecidos e Genes - Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, UFRGS, Porto Alegre, RS, Brazil; Departamento de Fisiologia, UFRGS, Porto Alegre, RS, Brazil
| | - Ursula Matte
- Laboratório de Células, Tecidos e Genes - Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, UFRGS, Porto Alegre, RS, Brazil; Departamento de Genética, UFRGS, Porto Alegre, RS, Brazil.
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Khatoon F, Kumar V, Anjum F, Shafie A, Adnan M, Hassan MI. Frustration analysis of TBK1 missense mutations reported in ALS/FTD and cancer patients. 3 Biotech 2022; 12:174. [PMID: 35845111 PMCID: PMC9283588 DOI: 10.1007/s13205-022-03240-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/23/2022] [Indexed: 11/29/2022] Open
Abstract
Tank-binding kinase 1 (TBK1) is a multifunctional kinase having essential roles in cellular processes, autophagy/mitophagy, and selective clearance of damaged proteins. More than 90 mutations in the TBK1 gene are linked with multiple cancer types, amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD). Some of these missense mutations disrupt the abilities of TBK1 to dimerize, associate with the mitophagy receptor optineurin (OPTN), autoactivate, or catalyze phosphorylation. Some mutations may cause severe dysregulation of the pathway, while others induce a limited disruption. Here, we have studied those mutations reported in cancer, ALS and FTD, and subsequently investigated the effect of missense mutations on the structure and function of TBK1 for localized residual frustration change. Out of 33 ALS/FTD causing mutations and 28 oncogenic mutations, 10 mutations and 12 oncogenic mutations showed significant change in the residual frustration. The local frustration plays an important role in the conformation of protein structure in active and inactive kinases. Our analysis reports the change in residual frustration state, conformational change and effect on active and inactive TBK1 function due to ALS/FTD causing and oncogenic missense mutations. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03240-0.
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Zahid S, Gul M, Shafique S, Rashid S. E2 UbcH5B-derived peptide ligands target HECT E3-E2 binding site and block the Ub-dependent SARS-CoV-2 egression: A computational study. Comput Biol Med 2022; 146:105660. [PMID: 35751189 PMCID: PMC9124161 DOI: 10.1016/j.compbiomed.2022.105660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/15/2022] [Accepted: 05/18/2022] [Indexed: 01/12/2023]
Abstract
Homologous to E6AP carboxyl-terminus (HECT)-type E3 ligase performs ubiquitin (Ub)-proteasomal protein degradation via forming a complex with E2∼Ub. Enveloped viruses including SARS-CoV-2 escape from the infected cells by harnessing the E-class vacuolar protein-sorting (ESCRT) machinery and mimic the cellular system through PPAY motif-based linking to HECT Ub ligase activity. In the present study, we have characterized the binding pattern of E2UbcH5B to HECT domains of NEDD4L, WWP1, WWP2, HECW1, and HECW2 through in silico analysis to isolate the E2UbcH5B-specific peptide inhibitors that may target SARS-CoV-2 viral egression. Molecular dynamics analysis revealed more opening of E2UbcH5B-binding pocket upon binding to HECTNEDD4L, HECTWWP1, HECTWWP2, HECTHECW1, and HECTHECW2. We observed similar binding pattern for E2UbcH5B and mentioned HECT domains as previously reported for HECTNEDD4L where Trp762, Trp709, and Trp657 residues of HECTNEDD4L, HECTWWP1, and HECTWWP2 are involved in making contacts with Ser94 residue of E2UbcH5B. Similarly, corresponding to HECTNEDD4L Tyr756 residue, HECTWWP1, HECTWWP2, HECTHECW1, and HECTHECW2-specific Phe703, Phe651, Phe1387, and Phe1353 residues execute interaction with E2UbcH5B. Our analysis suggests that corresponding to Cys942 of HECTNEDD4L, Cys890, Cys838, Cys1574, and Cys1540 residues of HECTWWP1, HECTWWP2, HECTHECW1, and HECTHECW2, respectively are involved in E2-to-E3 Ub transfer. Furthermore, MM-PBSA free energy calculations revealed favorable energy values for E2UbcH5B-HECT complexes along with the individual residue contributions. Subsequently, two E2UbcH5B-derived peptides (His55-Phe69 and Asn81-Ala96) were tested for their binding abilities against HECT domains of NEDD4L, WWP1, WWP2, HECW1, and HECW2. Their binding was validated through substitution of Phe62, Pro65, Ile84, and Cys85 residues into Ala, which revealed an impaired binding, suggesting that the proposed peptide ligands may selectively target E2-HECT binding and Ub-transfer. Collectively, we propose that peptide-driven blocking of E2-to-HECT Ub loading may limit SARS-CoV-2 egression and spread in the host cells.
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Ali F, Manzoor U, Khan FI, Lai D, Khan MKA, Chandrashekharaiah KS, Singh LR, Dar TA. Effect of polyol osmolytes on the structure-function integrity and aggregation propensity of catalase: A comprehensive study based on spectroscopic and molecular dynamic simulation measurements. Int J Biol Macromol 2022; 209:198-210. [PMID: 35395280 DOI: 10.1016/j.ijbiomac.2022.04.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/18/2022] [Accepted: 04/03/2022] [Indexed: 01/24/2023]
Abstract
Owing to the ability of catalase to function under oxidative stress vis-à-vis its industrial importance, the structure-function integrity of the enzyme is of prime concern. In the present study, polyols (glycerol, sorbitol, sucrose, xylitol), were evaluated for their ability to modulate structure, activity and aggregation of catalase using in vitro and in silico approaches. All polyols increased catalase activity by decreasing Km and increasing Vmax resulting in enhanced catalytic efficiency (kcat/Km) of the enzyme, with glycerol being the most efficient with a kcat/Km increase from 4.38 × 104 mM-1 S-1 (control) to 5.8 × 105 mM-1 S-1. Correlatively with this, enhanced secondary structure with reduced hydrophobic exposure was observed in all polyols. Furthermore, increased stability, with an increase in melting temperature by 15.2 °C, and almost no aggregation was observed in glycerol. Overall, ability to regulate structure-function integrity and aggregation propensity was highest for glycerol and lowest for xylitol. Simulation studies were performed involving structural dynamics measurements, principal component analysis and free energy landscape analysis. Altogether, all polyols were stabilizing in nature and glycerol, in particular, has potential to efficiently prevent not only the antioxidant defense system but also might serve as a stability aid during industrial processing of catalase.
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Affiliation(s)
- Fasil Ali
- Department of Studies and Research in Biochemistry, Jnana Kaveri Campus, Mangalore University, Karnataka 571232, India
| | - Usma Manzoor
- Department of Clinical Biochemistry, University of Kashmir, Srinagar 190006, Jammu and Kashmir, India
| | - Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Md Khurshid A Khan
- School of Life Sciences, B. S. Abdur Rahman Crescent Institute of Science and Technology, Vandalur, Chennai 600 048, Tamil Nadu, India
| | - K S Chandrashekharaiah
- Department of Studies and Research in Biochemistry, Jnana Kaveri Campus, Mangalore University, Karnataka 571232, India
| | | | - Tanveer Ali Dar
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
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Khan FI, Lobb KA, Lai D. The Molecular Basis of the Effect of Temperature on the Structure and Function of SARS-CoV-2 Spike Protein. Front Mol Biosci 2022; 9:794960. [PMID: 35463957 PMCID: PMC9019816 DOI: 10.3389/fmolb.2022.794960] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/27/2022] [Indexed: 12/14/2022] Open
Abstract
The remarkable rise of the current COVID-19 pandemic to every part of the globe has raised key concerns for the current public healthcare system. The spike (S) protein of SARS-CoV-2 shows an important part in the cell membrane fusion and receptor recognition. It is a key target for vaccine production. Several researchers studied the nature of this protein under various environmental conditions. In this work, we applied molecular modeling and extensive molecular dynamics simulation approaches at 0°C (273.15 K), 20°C (293.15 K), 40°C (313.15 K), and 60°C (333.15 K) to study the detailed conformational alterations in the SARS-CoV-2 S protein. Our aim is to understand the influence of temperatures on the structure, function, and dynamics of the S protein of SARS-CoV-2. The structural deviations, and atomic and residual fluctuations were least at low (0°C) and high (60°C) temperature. Even the internal residues of the SARS-CoV-2 S protein are not accessible to solvent at high temperature. Furthermore, there was no unfolding of SARS-CoV-2 spike S reported at higher temperature. The most stable conformations of the SARS-CoV-2 S protein were reported at 20°C, but the free energy minimum region of the SARS-CoV-2 S protein was sharper at 40°C than other temperatures. Our findings revealed that higher temperatures have little or no influence on the stability and folding of the SARS-CoV-2 S protein.
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Affiliation(s)
- Faez Iqbal Khan
- Department of Biological Sciences, School of Science, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Kevin A. Lobb
- Department of Chemistry, Rhodes University, Grahamstown, South Africa
- *Correspondence: Dakun Lai, ; Kevin A. Lobb,
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Dakun Lai, ; Kevin A. Lobb,
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11
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Jonniya NA, Sk MF, Roy R, Kar P. Discovery of potential competitive inhibitors against With-No-Lysine kinase 1 for treating hypertension by virtual screening, inverse pharmacophore-based lead optimization, and molecular dynamics simulations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:63-87. [PMID: 35078380 DOI: 10.1080/1062936x.2021.2023218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
The With-No-Lysine (WNK) has received attention because of its involvement in hypertension. Genetic mutation in the genes of WNK, leading to its overexpression, has been reported in Familial Hyperkalaemic Hypertension, and thus WNK is considered a potential drug target. Herein, we have performed a high-throughput virtual screening of ~11,000 compounds, mainly the natural phytochemical compounds and kinase inhibitory libraries, to find potential competitive inhibitors against WNK1. Initially, candidates with a docking score of ~ -10.0 kcal/mol or less were selected to further screen their good pharmacological properties by applying absorption, distribution, metabolism, excretion, and toxicity (ADMET). Finally, six docked compounds bearing appreciable binding affinities and WNK1 selectivity were complimented with 500 ns long all-atom molecular dynamic simulations. Subsequently, the MMPBSA scheme (Molecular Mechanics Poisson Boltzmann Surface Area) suggested three phytochemical compounds, C00000947, C00020451, and C00005031, with favourable binding affinity against WNK1. Among them, C00000947 acts as the most potent competitive inhibitor of WNK1. Further, inverse pharmacophore-based lead optimization of the C00000947 leads to one potential compound, meciadanol, which shows better binding affinity and specificity than C00000947 towards WNK1, which may be further exploited to develop effective therapeutics against WNK1-associated hypertension after in vitro and in vivo validation.
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Affiliation(s)
- N A Jonniya
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - M F Sk
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - R Roy
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - P Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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12
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Cheng KW, Tseng CH, Chen IJ, Huang BC, Liu HJ, Ho KW, Lin WW, Chuang CH, Huang MY, Leu YL, Roffler SR, Wang JY, Chen YL, Cheng TL. Inhibition of gut microbial β-glucuronidase effectively prevents carcinogen-induced microbial dysbiosis and intestinal tumorigenesis. Pharmacol Res 2022; 177:106115. [PMID: 35124207 DOI: 10.1016/j.phrs.2022.106115] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/13/2022] [Accepted: 02/01/2022] [Indexed: 01/11/2023]
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13
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Umair M, Khan S, Mohammad T, Shafie A, Anjum F, Islam A, Hassan MI. Impact of single amino acid substitution on the structure and function of TANK-binding kinase-1. J Cell Biochem 2021; 122:1475-1490. [PMID: 34237165 DOI: 10.1002/jcb.30070] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/26/2021] [Accepted: 05/31/2021] [Indexed: 12/14/2022]
Abstract
Tank-binding kinase 1 (TBK1) is a serine/threonine protein kinase involved in various signaling pathways and subsequently regulates cell proliferation, apoptosis, autophagy, antiviral and antitumor immunity. Dysfunction of TBK1 can cause many complex diseases, including autoimmunity, neurodegeneration, and cancer. This dysfunction of TBK1 may result from single amino acid substitutions and subsequent structural alterations. This study analyzed the effect of substituting amino acids on TBK1 structure, function, and subsequent disease using advanced computational methods and various tools. In the initial assessment, a total of 467 mutations were found to be deleterious. After that, in detailed structural and sequential analyses, 13 mutations were found to be pathogenic. Finally, based on the functional importance, two variants (K38D and S172A) of the TBK1 kinase domain were selected and studied in detail by utilizing all-atom molecular dynamics (MD) simulation for 200 ns. MD simulation, including correlation matrix and principal component analysis, helps to get deeper insights into the TBK1 structure at the atomic level. We observed a substantial change in variants' conformation, which may be possible for structural alteration and subsequent TBK1 dysfunction. However, substitution S172A shows a significant conformational change in TBK1 structure as compared to K38D. Thus, this study provides a structural basis to understand the effect of mutations on the kinase domain of TBK1 and its function associated with disease progression.
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Affiliation(s)
- Mohd Umair
- Department of Computer Science, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Shama Khan
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch, South Africa
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
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14
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Cheng J, Li X. Development and Application of Activity-based Fluorescent Probes for High-Throughput Screening. Curr Med Chem 2021; 29:1739-1756. [PMID: 34036907 DOI: 10.2174/0929867328666210525141728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 11/22/2022]
Abstract
High-throughput screening facilitates the rapid identification of novel hit compounds; however, it remains challenging to design effective high-throughput assays, partially due to the difficulty of achieving sensitivity in the assay techniques. Among the various analytical methods that are used, fluorescence-based assays dominate owing to their high sensitivity and ease of operation. Recent advances in activity-based sensing/imaging have further expanded the availability of fluorescent probes as monitors for high-throughput screening of result outputs. In this study, we have reviewed various activity-based fluorescent probes used in high-throughput screening assays, emphasizing their structure-related working mechanisms. Moreover, we have explored the possibility of the development of additional and better probes to boost hit identification and drug development against various targets.
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Affiliation(s)
- Juan Cheng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xin Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
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15
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Chen Y. Recent progress in natural product-based inhibitor screening with enzymatic fluorescent probes. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:1778-1787. [PMID: 33885636 DOI: 10.1039/d1ay00245g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Drug discovery is a complex process in which many challenges need to be overcome, from the discovery of a drug candidate to ensuring the efficacy and safety of the candidate in humans. Modern analytical methods allow tens of thousands of drug candidates to be screened for their inhibition of specific enzymes or receptors. In recent years, fluorescent probes have been used for the detection and diagnosis of human pathogens as well as high-throughput screening. This review focuses on recent progress in organic small-molecule based enzyme-activated fluorescent probes for screening of inhibitors from natural products. The contents include the construction of fluorescent probes, working mechanism and the process of inhibitor screening. The progress suggests that fluorescent probes are a vital and rapidly growing technology for inhibitor screening of enzymes, in particular, inhibitor screening in situ.
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Affiliation(s)
- Yi Chen
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China. and University of Chinese Academy of Sciences, Beijing, 100049, China
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16
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Shahbaaz M, Qari SH, Abdellattif MH, Hussien MA. Structural analyses and classification of novel isoniazid resistance coupled mutational landscapes in Mycobacterium tuberculosis: a combined molecular docking and MD simulation study. J Biomol Struct Dyn 2020; 40:4791-4800. [PMID: 33345744 DOI: 10.1080/07391102.2020.1861986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Drug resistance in Mycobacterium tuberculosis has become a major challenge to the current regime of treatment as well as to the containment of the disease globally. The molecular and genetic studies identified frequently occurring point mutations in the virulent protein such as KatG of M. tuberculosis resulted in the development of isoniazid tolerance in the pathogen. This study aims to analyze the structural basis of the disease mutations available in the literature as well as to predict novel alteration in the KatG which may cause similar deleterious effects. Around 15 experimentally derived mutations were included in this study and pathogenic mutational landscapes containing 60 site-specific alterations were predicted using the available in silico techniques. The effects of these mutations on the stability of the protein were studied and an exhaustive docking study was conducted for each classified perturbations, which identify the highest changes in the binding energies in p.Meth255Ile among experimental and p.Ala222Arg in computationally predicted mutations. Furthermore, the structural effects on these substitutions were analyzed using the principles of molecular dynamic simulations each for a 100 ns time scale, which validated the interaction studies. The outcome of this study may enable the identification of the novel drug resistance-associated point mutations which were not previously reported and may contribute significantly in a variety of experimental studies as well as facilitate the process of drug design and discovery.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohd Shahbaaz
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, Cape Town, South Africa.,Laboratory of Computational Modeling of Drugs, South Ural State University, Chelyabinsk, Russia
| | - Sameer H Qari
- Biology Department, Aljumum University College, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Magda H Abdellattif
- Department of Chemistry, College of Science, Deanship of Scientific Research, Taif University, Taif, Saudi Arabia
| | - Mostafa A Hussien
- Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Chemistry, Faculty of Science, Port Said University, Port Said, Egypt
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17
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Omolabi KF, Agoni C, Olotu FA, Soliman MES. Molecular Basis of P131 Cryptosporidial-IMPDH Selectivity-A Structural, Dynamical and Mechanistic Stance. Cell Biochem Biophys 2020; 79:11-24. [PMID: 33058015 DOI: 10.1007/s12013-020-00950-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2020] [Indexed: 01/10/2023]
Abstract
Cryptosporidiosis accounts for a surge in infant (<5 years) mortality and morbidity. To date, several drug discovery efforts have been put in place to develop effective therapeutic options against the causative parasite. Based on a recent report, P131 spares inosine monophosphate dehydrogenase (IMPDH) in a eukaryotic model (mouse IMPDH (mIMPDH)) while binding selectively to the NAD+ site in Cryptosporidium parvum (CpIMPDH). However, no structural detail exists on the underlining mechanisms of P131-CpIMPDH selective targeting till date. To this effect, we investigate the selective inhibitory dynamics of P131 in CpIMPDH relative to mIMPDH via molecular biocomputation methods. Pairwise sequence alignment revealed prominent variations at the NAD+ binding regions of both proteins that accounted for disparate P131 binding activities. The influence of these variations was further revealed by the MM/PBSA energy estimations coupled with per-residue energy decomposition which monitored the systematic binding of the compound. Furthermore, relative high-affinity interactions occurred at the CpIMPDH NAD+ site which were majorly mediated by SER22, VAL24, PRO26, SER354, GLY357, and TYR358 located on chain D. These residues are unique to the parasite IMPDH form and not in the eukaryotic protein, highlighting variations that account for preferential P131 binding. Molecular insights provided herein corroborate previous experimental reports and further underpin the basis of CpIMPDH inhibitor selectivity. Findings from this study could present attractive prospects toward the design of novel anticryptosporidials with improved selectivity and binding affinity against parasitic targets.
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Affiliation(s)
- Kehinde F Omolabi
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Clement Agoni
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Fisayo A Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.
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18
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Impact of amino acid substitution in the kinase domain of Bruton tyrosine kinase and its association with X-linked agammaglobulinemia. Int J Biol Macromol 2020; 164:2399-2408. [PMID: 32784026 DOI: 10.1016/j.ijbiomac.2020.08.057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/02/2020] [Accepted: 08/03/2020] [Indexed: 02/06/2023]
Abstract
X-linked agammaglobulinemia (XLA) is a rare disease that affects the immune system, characterized by a serial development of bacterial infection from the onset of infantile age. Bruton tyrosine kinase (BTK) is a non-receptor cytoplasmic kinase that plays a crucial role in the B-lymphocyte maturation. The altered expression, mutation and/or structural variations of BTK are responsible for causing XLA. Here, we have performed extensive sequence and structure analyses of BTK to find deleterious variations and their pathogenic association with XLA. First, we screened the pathogenic variations in the BTK from a pool of publicly available resources, and their pathogenicity/tolerance and stability predictions were carried out. Finally, two pathogenic variations (E589G and M630K) were studied in detail and subjected to all-atom molecular dynamics simulation for 200 ns. Intramolecular hydrogen bonds (H-bonds), secondary structure, and principal component analysis revealed significant conformational changes in variants that support the structural basis of BTK dysfunction in XLA. The free energy landscape analysis revealed the presence of multiple energy minima, suggests that E589G brings a large destabilization and consequently unfolding behavior compared to M630K. Overall, our study suggests that amino acid substitutions, E589G, and M630K, significantly alter the structural conformation and stability of BTK.
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19
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Uddin A, Singh V, Irfan I, Mohammad T, Singh Hada R, Imtaiyaz Hassan M, Abid M, Singh S. Identification and structure-activity relationship (SAR) studies of carvacrol derivatives as potential anti-malarial against Plasmodium falciparum falcipain-2 protease. Bioorg Chem 2020; 103:104142. [PMID: 32763521 DOI: 10.1016/j.bioorg.2020.104142] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/30/2020] [Accepted: 07/23/2020] [Indexed: 01/07/2023]
Abstract
In an effort to develop a potent anti-malarial agent against Plasmodium falciparum, a structure-guided virtual screening using an in-house library comprising 652 compounds was performed. By docking studies, we identified two compounds (JMI-105 and JMI-346) which formed significant non-covalent interactions and fit well in the binding pocket of PfFP-2. We affirmed this observation by MD simulation studies. As evident by the biochemical analysis, such as enzyme inhibition assay, Surface Plasmon Resonance (SPR), live-cell imaging and hemozoin inhibition, JMI-105 and JMI-346 at 25 µM concentration showed an inhibitory effect on purified PfFP-2. JMI-105 and JMI-346 inhibited the growth of CQS (3D7; IC50 = 8.8 and 13 µM) and CQR (RKL-9; IC50 = 14.3 and 33 µM) strains of P. falciparum. Treatment with compounds resulted in defect in parasite growth and development. No significant hemolysis or cytotoxicity towards human cells was observed suggesting that these molecules are non-toxic. We pursued, structural optimization on JMI-105 and in the process, SAR oriented derivatives (5a-5l) were synthesized and evaluated for growth inhibition potential. JMI-105 significantly decreased parasitemia and prolonged host survival in a murine model with P. berghei ANKA infection. The compounds (JMI-105 and JMI-346) against PfFP-2 have the potential to be used as an anti-malarial agent.
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Affiliation(s)
- Amad Uddin
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Vigyasa Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Iram Irfan
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Taj Mohammad
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Rahul Singh Hada
- Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh 201314, India
| | - Md Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India.
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20
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Jairajpuri D, Mohammad T, Adhikari K, Gupta P, Hasan GM, Alajmi MF, Rehman MT, Hussain A, Hassan MI. Identification of Sphingosine Kinase-1 Inhibitors from Bioactive Natural Products Targeting Cancer Therapy. ACS OMEGA 2020; 5:14720-14729. [PMID: 32596609 PMCID: PMC7315586 DOI: 10.1021/acsomega.0c01511] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/28/2020] [Indexed: 05/28/2023]
Abstract
Sphingosine kinase 1 (SphK1) is an oncogenic lipid kinase that catalyzes the formation of sphingosine-1-phosphate via phosphorylation of sphingosine and known to play a crucial role in angiogenesis, lymphocyte trafficking, signal transduction pathways, and response to apoptotic stimuli. SphK1 has received attention because of its involvement in varying types of cancer and inflammatory diseases such as rheumatoid arthritis, diabetes, renal fibrosis, pulmonary fibrosis, asthma, and neurodegenerative disorders. In the malignancies of breast, lung, uterus, ovary, kidney, and leukemia, overexpression of SphK1 has been reported and thus considered as a potential drug target. In this study, we have performed virtual high-throughput screening of ∼90,000 natural products from the ZINC database to find potential SphK1-inhibitors. Initially, the hits were selected by applying absorption, distribution, metabolism, excretion, and toxicity properties, Lipinski's rule, and PAINS filters. Further, docking analysis was performed to estimate the binding affinities and specificity to find safe and effective preclinical leads against SphK1. Two compounds, ZINC05434006 and ZINC04260971, bearing appreciable binding affinity and SphK1 selectivity were selected for 100 ns molecular dynamics (MD) simulations under explicit water conditions. The all-atom MD simulation results suggested that the ZINC05434006 and ZINC04260971 binding induces a slight structural change and stabilizes the SphK1 structure. In conclusion, we propose natural compounds, ZINC05434006 and ZINC04260971, as potential inhibitors of SphK1, which may be further exploited as potential leads to develop effective therapeutics against SphK1-associated diseases including cancer after in vitro and in vivo validations.
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Affiliation(s)
- Deeba
Shamim Jairajpuri
- Department
of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, P.O. Box 22971, Manama, Bahrain
| | - Taj Mohammad
- Center
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Kirtika Adhikari
- Department
of Computer Science, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Preeti Gupta
- Center
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Gulam Mustafa Hasan
- Department
of Biochemistry, College of Medicine, Prince
Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia
| | - Mohamed F. Alajmi
- Department
of Pharmacognosy, College of Pharmacy, King
Saud University, Riyadh 11451, Saudi Arabia
| | - Md. Tabish Rehman
- Department
of Pharmacognosy, College of Pharmacy, King
Saud University, Riyadh 11451, Saudi Arabia
| | - Afzal Hussain
- Department
of Pharmacognosy, College of Pharmacy, King
Saud University, Riyadh 11451, Saudi Arabia
| | - Md. Imtaiyaz Hassan
- Center
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
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21
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Naqvi AAT, Jairajpuri DS, Hussain A, Hasan GM, Alajmi MF, Hassan MI. Impact of glioblastoma multiforme associated mutations on the structure and function of MAP/microtubule affinity regulating kinase 4. J Biomol Struct Dyn 2020; 39:1781-1794. [DOI: 10.1080/07391102.2020.1738959] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ahmad Abu Turab Naqvi
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Deeba Shamim Jairajpuri
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Afzal Hussain
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, Kingdom of Saudi Arabia
| | - Mohamed F. Alajmi
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Md. Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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22
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Khan FI, Hassan F, Ali H, Lai D. Mechanism of pH-induced conformational changes in MurE ligase obtained from Salmonella enterica serovar Typhi. J Biomol Struct Dyn 2020; 39:1898-1905. [PMID: 32141393 DOI: 10.1080/07391102.2020.1739560] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Fakhrul Hassan
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Haider Ali
- Faculty of medicine, International Ala-too University, Bishkek, Kyrgyzstan
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
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23
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Hassan F, Khan FI, Song H, Lai D, Juan F. Effects of reverse genetic mutations on the spectral and photochemical behavior of a photoactivatable fluorescent protein PAiRFP1. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 228:117807. [PMID: 31806482 DOI: 10.1016/j.saa.2019.117807] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/29/2019] [Accepted: 11/15/2019] [Indexed: 06/10/2023]
Abstract
Bacteriophytochrome photoreceptors (BphPs) containing biliverdin (BV) have great potential for the development of genetically engineered near-infrared fluorescent proteins (NIR FPs). We investigated a photoactivatable fluorescent protein PAiRFP1, was engineered through directed molecular evolution. The coexistence of both red light absorbing (Pr) and far-red light absorbing (Pfr) states in dark is essential for the photoactivation of PAiRFP1. The PCR based site-directed reverse mutagenesis, spectroscopic measurements and molecular dynamics (MD) simulations were performed on three targeted sites V386A, V480A and Y498H in PHY domain to explore their potential effects during molecular evolution of PAiRFP1. We found that these substitutions did not affect the coexistence of Pr and Pfr states but led to slight changes in the photophysical parameters. The covalent docking of biliverdin (cis and trans form) with PAiRFP1 was followed by several 100 ns MD simulations to provide some theoretical explanations for the coexistence of Pr and pfr states. The results suggested that experimentally observed coexistence of Pr and Pfr states in both PAiRFP1 and mutants were resulted from the improved stability of Pr state. The use of experimental and computational work provided useful understanding of Pr and Pfr states and the effects of these mutations on the photophysical properties of PAiRFP1.
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Affiliation(s)
- Fakhrul Hassan
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China.
| | - Honghong Song
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China.
| | - Feng Juan
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.
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A Thermolabile Phospholipase B from Talaromyces marneffei GD-0079: Biochemical Characterization and Structure Dynamics Study. Biomolecules 2020; 10:biom10020231. [PMID: 32033124 PMCID: PMC7072546 DOI: 10.3390/biom10020231] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/20/2020] [Accepted: 01/28/2020] [Indexed: 12/01/2022] Open
Abstract
Phospholipase B (EC 3.1.1.5) are a distinctive group of enzymes that catalyzes the hydrolysis of fatty acids esterified at the sn-1 and sn-2 positions forming free fatty acids and lysophospholipids. The structural information and catalytic mechanism of phospholipase B are still not clear. Herein, we reported a putative phospholipase B (TmPLB1) from Talaromyces marneffei GD-0079 synthesized by genome mining library. The gene (TmPlb1) was expressed and the TmPLB1 was purified using E. coli shuffle T7 expression system. The putative TmPLB1 was purified by affinity chromatography with a yield of 13.5%. The TmPLB1 showed optimum activity at 35 °C and pH 7.0. The TmPLB1 showed enzymatic activity using Lecithin (soybean > 98% pure), and the hydrolysis of TmPLB1 by 31P NMR showed phosphatidylcholine (PC) as a major phospholipid along with lyso-phospholipids (1-LPC and 2-LPC) and some minor phospholipids. The molecular modeling studies indicate that its active site pocket contains Ser125, Asp183 and His215 as the catalytic triad. The structure dynamics and simulations results explained the conformational changes associated with different environmental conditions. This is the first report on biochemical characterization and structure dynamics of TmPLB1 enzyme. The present study could be helpful to utilize TmPLB1 in food industry for the determination of food components containing phosphorus. Additionally, such enzyme could also be useful in Industry for the modifications of phospholipids.
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Awolade P, Cele N, Kerru N, Gummidi L, Oluwakemi E, Singh P. Therapeutic significance of β-glucuronidase activity and its inhibitors: A review. Eur J Med Chem 2020; 187:111921. [PMID: 31835168 PMCID: PMC7111419 DOI: 10.1016/j.ejmech.2019.111921] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 11/27/2019] [Accepted: 11/27/2019] [Indexed: 01/02/2023]
Abstract
The emergence of disease and dearth of effective pharmacological agents on most therapeutic fronts, constitutes a major threat to global public health and man's existence. Consequently, this has created an exigency in the search for new drugs with improved clinical utility or means of potentiating available ones. To this end, accumulating empirical evidence supports molecular target therapy as a plausible egress and, β-glucuronidase (βGLU) - a lysosomal acid hydrolase responsible for the catalytic deconjugation of β-d-glucuronides has emerged as a viable molecular target for several therapeutic applications. The enzyme's activity level in body fluids is also deemed a potential biomarker for the diagnosis of some pathological conditions. Moreover, due to its role in colon carcinogenesis and certain drug-induced dose-limiting toxicities, the development of potent inhibitors of βGLU in human intestinal microbiota has aroused increased attention over the years. Nevertheless, although our literature survey revealed both natural products and synthetic scaffolds as potential inhibitors of the enzyme, only few of these have found clinical utility, albeit with moderate to poor pharmacokinetic profile. Hence, in this review we present a compendium of exploits in the present millennium directed towards the inhibition of βGLU. The aim is to proffer a platform on which new scaffolds can be modelled for improved βGLU inhibitory potency and the development of new therapeutic agents in consequential.
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Affiliation(s)
- Paul Awolade
- School of Chemistry and Physics, University of KwaZulu-Natal, P/Bag X54001, Westville, Durban, South Africa
| | - Nosipho Cele
- School of Chemistry and Physics, University of KwaZulu-Natal, P/Bag X54001, Westville, Durban, South Africa
| | - Nagaraju Kerru
- School of Chemistry and Physics, University of KwaZulu-Natal, P/Bag X54001, Westville, Durban, South Africa
| | - Lalitha Gummidi
- School of Chemistry and Physics, University of KwaZulu-Natal, P/Bag X54001, Westville, Durban, South Africa
| | - Ebenezer Oluwakemi
- School of Chemistry and Physics, University of KwaZulu-Natal, P/Bag X54001, Westville, Durban, South Africa
| | - Parvesh Singh
- School of Chemistry and Physics, University of KwaZulu-Natal, P/Bag X54001, Westville, Durban, South Africa.
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Khan FI, Lai D, Anwer R, Azim I, Khan MKA. Identifying novel sphingosine kinase 1 inhibitors as therapeutics against breast cancer. J Enzyme Inhib Med Chem 2020; 35:172-186. [PMID: 31752564 PMCID: PMC6882459 DOI: 10.1080/14756366.2019.1692828] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Sphingosine kinase 1 (SphK1) is a promising therapeutic target against several diseases including mammary cancer. The aim of present work is to identify a potent lead compound against breast cancer using ligand-based virtual screening, molecular docking, MD simulations, and the MMPBSA calculations. The LBVS in molecular and virtual libraries yielded 20,800 hits, which were reduced to 621 by several parameters of drug-likeness, lead-likeness, and PAINS. Furthermore, 55 compounds were selected by ADMET descriptors carried forward for molecular interaction studies with SphK1. The binding energy (ΔG) of three screened compounds namely ZINC06823429 (–11.36 kcal/mol), ZINC95421501 (–11.29 kcal/mol), and ZINC95421070 (–11.26 kcal/mol) exhibited stronger than standard drug PF-543 (–9.9 kcal/mol). Finally, it was observed that the ZINC06823429 binds tightly to catalytic site of SphK1 and remain stable during MD simulations. This study provides a significant understanding of SphK1 inhibitors that can be used in the development of potential therapeutics against breast cancer.
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Affiliation(s)
- Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Razique Anwer
- Department of Pathology, College of Medicine, Imam Mohammad ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Iffat Azim
- Department of Bioengineering, Faculty of Engineering, Integral University, Lucknow, India
| | - Mohd Kalim Ahmad Khan
- Department of Bioengineering, Faculty of Engineering, Integral University, Lucknow, India
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Losada Díaz JC, Cepeda del Castillo J, Rodriguez-López EA, Alméciga-Díaz CJ. Advances in the Development of Pharmacological Chaperones for the Mucopolysaccharidoses. Int J Mol Sci 2019; 21:ijms21010232. [PMID: 31905715 PMCID: PMC6981736 DOI: 10.3390/ijms21010232] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/21/2019] [Accepted: 11/25/2019] [Indexed: 12/20/2022] Open
Abstract
The mucopolysaccharidoses (MPS) are a group of 11 lysosomal storage diseases (LSDs) produced by mutations in the enzymes involved in the lysosomal catabolism of glycosaminoglycans. Most of the mutations affecting these enzymes may lead to changes in processing, folding, glycosylation, pH stability, protein aggregation, and defective transport to the lysosomes. It this sense, it has been proposed that the use of small molecules, called pharmacological chaperones (PCs), can restore the folding, trafficking, and biological activity of mutated enzymes. PCs have the advantages of wide tissue distribution, potential oral administration, lower production cost, and fewer issues of immunogenicity than enzyme replacement therapy. In this paper, we will review the advances in the identification and characterization of PCs for the MPS. These molecules have been described for MPS II, IVA, and IVB, showing a mutation-dependent enhancement of the mutated enzymes. Although the results show the potential of this strategy, further studies should focus in the development of disease-specific cellular models that allow a proper screening and evaluation of PCs. In addition, in vivo evaluation, both pre-clinical and clinical, should be performed, before they can become a real therapeutic strategy for the treatment of MPS patients.
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Affiliation(s)
- Juan Camilo Losada Díaz
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá D.C. 110231, Colombia; (J.C.L.D.); (J.C.d.C.); (E.A.R.-L.)
| | - Jacobo Cepeda del Castillo
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá D.C. 110231, Colombia; (J.C.L.D.); (J.C.d.C.); (E.A.R.-L.)
| | - Edwin Alexander Rodriguez-López
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá D.C. 110231, Colombia; (J.C.L.D.); (J.C.d.C.); (E.A.R.-L.)
- Chemistry Department, Faculty of Science, Pontificia Universidad Javeriana, Bogotá D.C. 110231, Colombia
| | - Carlos J. Alméciga-Díaz
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá D.C. 110231, Colombia; (J.C.L.D.); (J.C.d.C.); (E.A.R.-L.)
- Correspondence: ; Tel.: +57-1-3208320 (ext. 4140); Fax: +57-1-3208320 (ext. 4099)
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Mohammad T, Batra S, Dahiya R, Baig MH, Rather IA, Dong JJ, Hassan I. Identification of High-Affinity Inhibitors of Cyclin-Dependent Kinase 2 Towards Anticancer Therapy. Molecules 2019; 24:E4589. [PMID: 31847444 PMCID: PMC6943647 DOI: 10.3390/molecules24244589] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 01/10/2023] Open
Abstract
Cyclin-dependent kinase 2 (CDK2) is an essential protein kinase involved in the cell cycle regulation. The abnormal activity of CDK2 is associated with cancer progression and metastasis. Here, we have performed structure-based virtual screening of the PubChem database to identify potent CDK2 inhibitors. First, we retrieved all compounds from the PubChem database having at least 90% structural similarity with the known CDK2 inhibitors. The selected compounds were subjected to structure-based molecular docking studies to investigate their pattern of interaction and estimate their binding affinities with CDK2. Selected compounds were further filtered out based on their physicochemical and ADMET properties. Detailed interaction analysis revealed that selected compounds interact with the functionally important residues of the active site pocket of CDK2. All-atom molecular dynamics simulation was performed to evaluate conformational changes, stability and the interaction mechanism of CDK2 in-complex with the selected compound. We found that binding of 6-N,6-N-dimethyl-9-(2-phenylethyl)purine-2,6-diamine stabilizes the structure of CDK2 and causes minimal conformational change. Finally, we suggest that the compound (PubChem ID 101874157) would be a promising scaffold to be further exploited as a potential inhibitor of CDK2 for therapeutic management of cancer after required validation.
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Affiliation(s)
- Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India; (T.M.); (R.D.)
| | - Sagar Batra
- Amity Institute of Biotechnology, Amity University Rajasthan, Rajasthan 303002, India;
| | - Rashmi Dahiya
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India; (T.M.); (R.D.)
| | - Mohammad Hassan Baig
- Department of Family Medicine, Yonsei University College of Medicine, Gangnam Severance Hospital, 211 Eonju-Ro, Gangnam-Gu, Seoul 06273, Korea; (M.H.B.); (J.-J.D.)
| | - Irfan Ahmad Rather
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80141, Jeddah 21589, Saudi Arabia;
| | - Jae-June Dong
- Department of Family Medicine, Yonsei University College of Medicine, Gangnam Severance Hospital, 211 Eonju-Ro, Gangnam-Gu, Seoul 06273, Korea; (M.H.B.); (J.-J.D.)
| | - Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India; (T.M.); (R.D.)
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Gupta P, Mohammad T, Dahiya R, Roy S, Noman OMA, Alajmi MF, Hussain A, Hassan MI. Evaluation of binding and inhibition mechanism of dietary phytochemicals with sphingosine kinase 1: Towards targeted anticancer therapy. Sci Rep 2019; 9:18727. [PMID: 31822735 PMCID: PMC6904568 DOI: 10.1038/s41598-019-55199-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/08/2019] [Indexed: 12/13/2022] Open
Abstract
Sphingosine kinase 1 (SphK1) has recently gained attention as a potential drug target for its association with cancer and other inflammatory diseases. Here, we have investigated the binding affinity of dietary phytochemicals viz., ursolic acid, capsaicin, DL-α tocopherol acetate, quercetin, vanillin, citral, limonin and simvastatin with the SphK1. Docking studies revealed that all these compounds bind to the SphK1 with varying affinities. Fluorescence binding and isothermal titration calorimetric measurements suggested that quercetin and capsaicin bind to SphK1 with an excellent affinity, and significantly inhibits its activity with an admirable IC50 values. The binding mechanism of quercetin was assessed by docking and molecular dynamics simulation studies for 100 ns in detail. We found that quercetin acts as a lipid substrate competitive inhibitor, and it interacts with important residues of active-site pocket through hydrogen bonds and other non-covalent interactions. Quercetin forms a stable complex with SphK1 without inducing any significant conformational changes in the protein structure. In conclusion, we infer that quercetin and capsaicin provide a chemical scaffold to develop potent and selective inhibitors of SphK1 after required modifications for the clinical management of cancer.
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Affiliation(s)
- Preeti Gupta
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Rashmi Dahiya
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Sonam Roy
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Omar Mohammed Ali Noman
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Mohamed F Alajmi
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia.
| | - Afzal Hussain
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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Dubot P, Sabourdy F, Plat G, Jubert C, Cancès C, Broué P, Touati G, Levade T. First Report of a Patient with MPS Type VII, Due to Novel Mutations in GUSB, Who Underwent Enzyme Replacement and Then Hematopoietic Stem Cell Transplantation. Int J Mol Sci 2019; 20:ijms20215345. [PMID: 31661765 PMCID: PMC6861985 DOI: 10.3390/ijms20215345] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 11/25/2022] Open
Abstract
We report the case of a boy who was diagnosed with mucopolysaccharidosis (MPS) VII at two weeks of age. He harbored three missense β-glucuronidase (GUSB) variations in exon 3: two novel, c.422A>C and c.424C>T, inherited from his mother, and the rather common c.526C>T, inherited from his father. Expression of these variations in transfected HEK293T cells demonstrated that the double mutation c.422A>C;424C>T reduces β-glucuronidase enzyme activity. Enzyme replacement therapy (ERT), using UX003 (vestronidase alfa), was started at four months of age, followed by a hematopoietic stem cell allograft transplantation (HSCT) at 13 months of age. ERT was well tolerated and attenuated visceromegaly and skin infiltration. After a severe skin and gut graft-versus-host disease, ERT was stopped six months after HSCT. The last follow-up examination (at the age of four years) revealed a normal psychomotor development, stabilized growth curve, no hepatosplenomegaly, and no other organ involvement. Intriguingly, enzyme activity had normalized in leukocytes but remained low in plasma. This case report illustrates: (i) The need for an early diagnosis of MPS, and (ii) the possible benefit of a very early enzymatic and/or cellular therapy in this rare form of lysosomal storage disease.
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Affiliation(s)
- Patricia Dubot
- Laboratoire de Biochimie Métabolique, Centre de Référence en Maladies Héréditaires du Métabolisme, Institut Fédératif de Biologie, CHU de Toulouse, 31059 Toulouse cedex 9, France.
- INSERM UMR1037, CRCT (Cancer Research Center of Toulouse), Université Paul Sabatier, 31037 Toulouse, France.
| | - Frédérique Sabourdy
- Laboratoire de Biochimie Métabolique, Centre de Référence en Maladies Héréditaires du Métabolisme, Institut Fédératif de Biologie, CHU de Toulouse, 31059 Toulouse cedex 9, France.
- INSERM UMR1037, CRCT (Cancer Research Center of Toulouse), Université Paul Sabatier, 31037 Toulouse, France.
| | - Geneviève Plat
- Service d'Hématologie Pédiatrique, CHU de Toulouse, 31058 Toulouse, France.
| | - Charlotte Jubert
- Service d'Hématologie Pédiatrique, CHU de Bordeaux, 33076 Bordeaux, France.
| | - Claude Cancès
- Hôpital des Enfants, Centre de Référence en Maladies Héréditaires du Métabolisme, CHU de Toulouse, 31059 Toulouse, France.
| | - Pierre Broué
- Hôpital des Enfants, Centre de Référence en Maladies Héréditaires du Métabolisme, CHU de Toulouse, 31059 Toulouse, France.
| | - Guy Touati
- Hôpital des Enfants, Centre de Référence en Maladies Héréditaires du Métabolisme, CHU de Toulouse, 31059 Toulouse, France.
| | - Thierry Levade
- Laboratoire de Biochimie Métabolique, Centre de Référence en Maladies Héréditaires du Métabolisme, Institut Fédératif de Biologie, CHU de Toulouse, 31059 Toulouse cedex 9, France.
- INSERM UMR1037, CRCT (Cancer Research Center of Toulouse), Université Paul Sabatier, 31037 Toulouse, France.
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Fatima S, Mohammad T, Jairajpuri DS, Rehman MT, Hussain A, Samim M, Ahmad FJ, Alajmi MF, Hassan MI. Identification and evaluation of glutathione conjugate gamma-l-glutamyl-l-cysteine for improved drug delivery to the brain. J Biomol Struct Dyn 2019; 38:3610-3620. [PMID: 31496427 DOI: 10.1080/07391102.2019.1664937] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Glutathione (GU), an endogenous antioxidant tripeptide, is frequently transferred in the human brain through N-methyl-d-aspartate receptor (NMDAR), profusely expressed at the blood-brain barrier (BBB) junction. GU, also modifies the characteristics of tight junction proteins (occludin and claudin) at the site of BBB by depolarizing the enzyme, protein tyrosine phosphatase that manifests its usefulness for passive delivery of nanocarriers to the brain. GU, thus, represents itself as an ideal ligand for the surface decoration of nanocarriers to successfully administer them across the brain via receptor-mediated drug delivery pathway. Hence, we have employed here, in-silico approaches to identify the potential GU-like molecules, as appropriate ligand(s) for surface engineering of nanoconstruct with the purpose of attaining targeted drug delivery to the brain. Structure-based virtual screening methods was used to filter PubChem database for the identification of bioactive compounds with >95% structure similarity with GU. We have further screened the compounds against NMDAR using molecular docking approach. Top hits were selected based on their high binding affinities and selectivity towards NMDAR, and their binding pattern was analysed in detail. Finally, all atom molecular dynamics simulation for 100 ns was carried out on free NMDAR and in-presence of the selected GU-like compound, gamma-l-glutamyl-l-cysteine to evaluate complex stability and structural dynamics. In conclusion, gamma-l-glutamyl-l-cysteine may act as potential binding partner of NMDAR which can further be evaluated in drug delivery system to brain across the BBB.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saman Fatima
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Deeba Shamim Jairajpuri
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Samim
- Department of Chemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Farhan Jalees Ahmad
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Mohammed F Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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Dahiya R, Mohammad T, Gupta P, Haque A, Alajmi MF, Hussain A, Hassan MI. Molecular interaction studies on ellagic acid for its anticancer potential targeting pyruvate dehydrogenase kinase 3. RSC Adv 2019; 9:23302-23315. [PMID: 35514501 PMCID: PMC9067284 DOI: 10.1039/c9ra02864a] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/15/2019] [Indexed: 11/21/2022] Open
Abstract
Pyruvate dehydrogenase kinase 3 (PDK3) plays a central role in the cancer metabolic switch through the reversible phosphorylation of pyruvate dehydrogenase complex thereby blocking the entry of pyruvate for its catabolism into the TCA cycle, and thus it is considered as an important drug target for various types of cancers. We have successfully expressed full length human PDK3 and investigated its interaction mechanism with dietary polyphenols in the search for potential inhibitors. Molecular docking analysis revealed that the selected compounds preferentially bind to the ATP-binding pocket of PDK3 and interact with functionally important residues. In silico observations were further complemented by experimental measurements of the fluorescence quenching of PDK3 and confirmed with the isothermal titration calorimetry measurements. Ellagic acid (EA) significantly binds and inhibits the kinase activity of PDK3. In vitro cytotoxicity and the anti-proliferative properties of EA were evaluated by MTT assay. Conformational dynamics of the EA-PDK3 complex during molecular dynamics simulation revealed that a stable complex was maintained by a significant number of hydrogen bonds throughout the 100 ns trajectories. In conclusion, EA may be considered as a promising molecule for PDK3 inhibition and could be exploited as a lead molecule against PDK3 associated diseases.
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Affiliation(s)
- Rashmi Dahiya
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia Jamia Nagar New Delhi 110025 India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia Jamia Nagar New Delhi 110025 India
| | - Preeti Gupta
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia Jamia Nagar New Delhi 110025 India
| | - Anzarul Haque
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia Jamia Nagar New Delhi 110025 India
| | - Mohamed F Alajmi
- Department of Pharmacognosy College of Pharmacy, King Saud University Riyadh 11451 Kingdom of Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy College of Pharmacy, King Saud University Riyadh 11451 Kingdom of Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia Jamia Nagar New Delhi 110025 India
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Chamseddine AN, Ducreux M, Armand JP, Paoletti X, Satar T, Paci A, Mir O. Intestinal bacterial β-glucuronidase as a possible predictive biomarker of irinotecan-induced diarrhea severity. Pharmacol Ther 2019; 199:1-15. [DOI: 10.1016/j.pharmthera.2019.03.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Naqvi AAT, Alajmi MF, Rehman T, Hussain A, Hassan I. Effects of Pro1266Leu mutation on structure and function of glycoprotein Ib binding domain of von Willebrand factor. J Cell Biochem 2019; 120:17847-17857. [PMID: 31135071 DOI: 10.1002/jcb.29052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 02/06/2023]
Abstract
Glycoprotein Ibα (GpIbα) binding ability of A1 domain of von Willebrand factor (vWF) facilitates platelet adhesion that plays a crucial role in maintaining hemostasis and thrombosis at the site of vascular damage. There are both "loss as well as gain of function" mutations observed in this domain. Naturally occurring "gain of function" mutations leave self-activating impacts on the A1 domain which turns the normal binding to characteristic constitutive binding with GPIbα. These "gain of function" mutations are associated with the von Willebrand disease type 2B. In recent years, studies focused on understanding the mechanism and conformational patterns attached to these phenomena have been conducted, but the conformational pathways leading to such binding patterns are poorly understood as of now. To obtain a microscopic picture of such events for the better understanding of pathways, we used molecular dynamics (MD) simulations along with principal component analysis and normal mode analysis to study the effects of Pro1266Leu (Pro503Leu in structural context) mutation on the structure and function of A1 domain of vWF. MD simulations have provided atomic-level details of intermolecular motions as a function of time to understand the dynamic behavior of A1 domain of vWF. Comparative analysis of the trajectories obtained from MD simulations of both the wild type and Pro503Leu mutant suggesting appreciable conformational changes in the structure of mutant which might provide a basis for assuming the "gain of function" effects of these mutations on the A1 domain of vWF, resulting in the constitutive binding with GpIbα.
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Affiliation(s)
- Ahmad Abu Turab Naqvi
- Center for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Mohamed F Alajmi
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, KSA
| | - Tabish Rehman
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, KSA
| | - Afzal Hussain
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, KSA
| | - Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
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35
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Ali S, Khan FI, Mohammad T, Lan D, Hassan MI, Wang Y. Identification and Evaluation of Inhibitors of Lipase from Malassezia restricta using Virtual High-Throughput Screening and Molecular Dynamics Studies. Int J Mol Sci 2019; 20:ijms20040884. [PMID: 30781686 PMCID: PMC6412828 DOI: 10.3390/ijms20040884] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/09/2019] [Accepted: 02/13/2019] [Indexed: 02/06/2023] Open
Abstract
Recent studies revealed the role of lipase in the pathogenicity of Malassezia restricta in dandruff and seborrheic dermatitis (D/SD). The lipase from M. restricta (Mrlip1) is considered a potential target for dandruff therapy. In this work, we performed structure-based virtual screening in Zinc database to find the natural bioactive inhibitors of Mrlip1. We identified three compounds bearing superior affinity and specificity from the Traditional Chinese Medicine database (~60,000 compounds), and their binding patterns with Mrlip1 were analyzed in detail. Additionally, we performed three sets of 100 ns MD simulations of each complex in order to understand the interaction mechanism of Mrlip1 with known inhibitor RHC80267 and the newly identified compounds such as ZINC85530919, ZINC95914464 and ZINC85530320, respectively. These compounds bind to the active site cavity and cause conformational changes in Mrlip1. The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) studies suggested that the average binding energy was stronger in the case of Mrlip1-ZINC85530919 and Mrlip1-ZINC95914464. The selected natural inhibitors might act as promising lead drugs against Mrlip1. Further, the present study will contribute to various steps involved in developing and creating potent drugs for several skin diseases including dandruff.
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Affiliation(s)
- Shahid Ali
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China.
| | - Faez Iqbal Khan
- Department of Chemistry, Rhodes University, Grahamstown 6140, South Africa.
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi-110025, India.
| | - Dongming Lan
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China.
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi-110025, India.
| | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China.
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X-Ray Crystallography in Structure-Function Characterization of Therapeutic Enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1148:81-103. [DOI: 10.1007/978-981-13-7709-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Structural basis for renal cancer by the dynamics of pVHL-dependent JADE1 stabilization and β-catenin regulation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 145:65-77. [PMID: 30528740 DOI: 10.1016/j.pbiomolbio.2018.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/19/2018] [Accepted: 12/06/2018] [Indexed: 11/21/2022]
Abstract
Renal cancer is the major cause of mortality due to abnormal functioning of von Hippel-Lindau (pVHL) and Jade Family PHD Finger 1 (JADE1) complex. E3 ubiquitin ligase JADE1 is stabilized by pVHL interaction through its plant homeodomains (PHDs). JADE1 acts as a renal tumor suppressor that promotes the ubiquitination and degradation of β-catenin by inhibiting canonical WNT signalling. Current study focuses on the structural characterization of reported missense mutations in pVHL through in silico approaches. The predicted 3-dimensional structures of pVHLWT, pVHLY98H, pVHLY112H, pVHLL118P and pVHLR167W were subjected to binding analysis against JADE1 through molecular docking and simulation assays. In all cases, JADE1 binding was observed at the β-domain, except pVHLL118P that exhibited binding with JADE1 through its α-domain. Our results signify that JADE1 stabilization is induced by pVHL α-domain, while β-domain is required for JADE1 binding. pVHL binding was mediated through β1 and β2-strands against the concave surface of the JADE1-PHD domain. The pVHL-JADE1 complex was evaluated to scrutinize the β-catenin-binding interface, which suggested the contribution of both α and β-domains of pVHL in β-catenin binding. The eleven-residue (Tyr30-Thr40) β-catenin segment exhibited association in a bipartite manner with pVHL-JADE1 complex. The presented model depicts a pVHL-JADE1 interface for the cooperative regulation of β-catenin binding. We propose that reduced JADE1 stabilization in case of pVHLL118P and pVHLR167W may correlate with the increased activity of β-catenin that may lead to renal cancer through β-catenin de-repression. Overall, β-catenin targeting mechanism coupled with the structural knowledge of JADE1-pVHL complex will provide better understanding of renal cancer pathogenesis.
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Beg A, Khan FI, Lobb KA, Islam A, Ahmad F, Hassan MI. High throughput screening, docking, and molecular dynamics studies to identify potential inhibitors of human calcium/calmodulin-dependent protein kinase IV. J Biomol Struct Dyn 2018; 37:2179-2192. [PMID: 30044185 DOI: 10.1080/07391102.2018.1479310] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Calcium/calmodulin-dependent protein kinase IV (CAMKIV) is associated with many diseases including cancer and neurodegenerative disorders and thus being considered as a potential drug target. Here, we have employed the knowledge of three-dimensional structure of CAMKIV to identify new inhibitors for possible therapeutic intervention. We have employed virtual high throughput screening of 12,500 natural compounds of Zinc database to screen the best possible inhibitors of CAMKIV. Subsequently, 40 compounds which showed significant docking scores (-11.6 to -10.0 kcal/mol) were selected and further filtered through Lipinski rule and drug likeness parameter to get best inhibitors of CAMKIV. Docking results are indicating that ligands are binding to the hydrophobic cavity of the kinase domain of CAMKIV and forming a significant number of non-covalent interactions. Four compounds, ZINC02098378, ZINC12866674, ZINC04293413, and ZINC13403020, showing excellent binding affinity and drug likeness were subjected to molecular dynamics simulation to evaluate their mechanism of interaction and stability of protein-ligand complex. Our observations clearly suggesting that these selected ligands may be further employed for therapeutic intervention to address CAMKIV associated diseases. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anam Beg
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi , India
| | - Faez Iqbal Khan
- b Computational Mechanistic Chemistry and Drug Discovery , Rhodes University , Grahamstown , South Africa
| | - Kevin A Lobb
- b Computational Mechanistic Chemistry and Drug Discovery , Rhodes University , Grahamstown , South Africa
| | - Asimul Islam
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi , India
| | - Faizan Ahmad
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi , India
| | - Md Imtaiyaz Hassan
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi , India
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Husain FM, Ahmad I, Khan FI, Al-Shabib NA, Baig MH, Hussain A, Rehman MT, Alajmi MF, Lobb KA. Seed Extract of Psoralea corylifolia and Its Constituent Bakuchiol Impairs AHL-Based Quorum Sensing and Biofilm Formation in Food- and Human-Related Pathogens. Front Cell Infect Microbiol 2018; 8:351. [PMID: 30410871 PMCID: PMC6211212 DOI: 10.3389/fcimb.2018.00351] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 09/14/2018] [Indexed: 01/18/2023] Open
Abstract
The emergence of multi-drug resistance in pathogenic bacteria in clinical settings as well as food-borne infections has become a serious health concern. The problem of drug resistance necessitates the need for alternative novel therapeutic strategies to combat this menace. One such approach is targeting the quorum-sensing (QS) controlled virulence and biofilm formation. In this study, we first screened different fractions of Psoralea corylifolia (seed) for their anti-QS property in the Chromobacterium violaceum 12472 strain. The methanol fraction was found to be the most active fraction and was selected for further bioassays. At sub-inhibitory concentrations, the P. corylifolia methanol fraction (PCMF) reduced QS-regulated virulence functions in C. violaceum CVO26 (violacein); Pseudomonas aeruginosa (elastase, protease, pyocyanin, chitinase, exopolysaccharides (EPS), and swarming motility), A. hydrophila (protease, EPS), and Serratia marcescens (prodigiosin). Biofilm formation in all the test pathogens was reduced significantly (p ≤ 0.005) in a concentration-dependent manner. The β-galactosidase assay showed that the PCMF at 1,000 μg/ml downregulated las-controlled transcription in PAO1. In vivo studies with C. elegans demonstrated increased survival of the nematodes after treatment with the PCMF. Bakuchiol, a phytoconstituent of the extract, demonstrated significant inhibition of QS-regulated violacein production in C. violaceum and impaired biofilm formation in the test pathogens. The molecular docking results suggested that bakuchiol efficiently binds to the active pockets of LasR and RhlR, and the complexes were stabilized by several hydrophobic interactions. Additionally, the molecular dynamics simulation of LasR, LasR-bakuchiol, RhlR, and RhlR-bakuchiol complexes for 50 ns revealed that the binding of bakuchiol to LasR and RhlR was fairly stable. The study highlights the anti-infective potential of the PCMF and bakuchiol instead of bactericidal or bacteriostatic action, as the extract targets QS-controlled virulence and the biofilm.
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Affiliation(s)
- Fohad Mabood Husain
- Department of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia.,Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, India
| | - Iqbal Ahmad
- Department of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Faez Iqbal Khan
- Department of Chemistry, Rhodes University, Grahamstown, South Africa
| | - Nasser A Al-Shabib
- Department of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | | | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed F Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Kevin A Lobb
- Department of Chemistry, Rhodes University, Grahamstown, South Africa
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40
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Amir M, Kumar V, Dohare R, Islam A, Ahmad F, Hassan MI. Sequence, structure and evolutionary analysis of cold shock domain proteins, a member of OB fold family. J Evol Biol 2018; 31:1903-1917. [PMID: 30267552 DOI: 10.1111/jeb.13382] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 11/28/2022]
Abstract
The cold shock domain (CSD) belongs to the oligosaccharide/oligonucleotide-binding fold superfamily which is highly conserved from prokaryotes to higher eukaryotes, and appears to function as RNA chaperones. CSD is involved in diverse cellular processes, including adaptation to low temperatures, nutrient stress, cellular growth and developmental processes. Structural Classification of Proteins (SCOP) database broadly classifies OB fold proteins into 18 different superfamilies, including nucleic acid-binding superfamily (NAB). The NAB is further divided into 17 families together with cold shock DNA-binding protein family (CSDB). The CSDB have more than 240 000 sequences in UniProt database consisting of 32 domains including CSD. Among these domains, CSD is the second largest sequence contributor (> 40 398 sequences). Herein, we have systematically analysed the relative abundance and distribution of CSD proteins based on sequences, structures, repeats and gene ontology (GO) molecular functions in all domains of life. Analysis of sequence distribution suggesting that CSDs are largely found in bacteria (83-94%) with single CSD repeat. However, repeat distribution in eukaryota varies from 1 to 5 in combination with other auxiliary domain that makes CSD proteins functionally more diverse compared to the bacterial counterparts. Further, analysis of repeats distributions on evolutionary scale suggest that existence of CSD in multiple repeats is mainly driven through speciation, gene shuffling and gene duplication events.
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Affiliation(s)
- Mohd Amir
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Vijay Kumar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.,Amity Institute of Neuropsychology & Neurosciences, Amity University Noida, UP, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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41
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Feng L, Yang Y, Huo X, Tian X, Feng Y, Yuan H, Zhao L, Wang C, Chu P, Long F, Wang W, Ma X. Highly Selective NIR Probe for Intestinal β-Glucuronidase and High-Throughput Screening Inhibitors to Therapy Intestinal Damage. ACS Sens 2018; 3:1727-1734. [PMID: 30149692 DOI: 10.1021/acssensors.8b00471] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
β-Glucuronidase (GLU) as a vital factor in enterohepatic circulation and drug-inducing enteropathy has been given more and more attention in recent years. In this study, an off-on near-infrared (NIR) fluorescent probe (DDAO-glu) for selectively and sensitively sensing GLU was developed on the basis of its substrate preference. DDAO-glu can rapidly and selectively respond to bacterial GLU under physiological conditions for detecting the real-time intestinal GLU bioactivity of complex biological systems such as human feces in clinic. Meantime, DDAO-glu has been successfully applied for visualization of endogenous GLU in bacterial biofilm, thallus, and even in vivo. Using this NIR probe, we successfully visualized the real distribution of intestinal GLU in the enterohepatic circulation. Furthermore, a high-throughput screening method was successfully established by our probe, and a potent natural inhibitor of GLU was identified as (-)-epicatechin-3-gallate (ECG) for effectively preventing NSAIDs-inducing enteropathy in vivo. DDAO-glu could serve as a powerful tool for exploring real physical functions of intestinal GLU in enterohepatic circulation, under physiological and pathological contexts, and developing the novel inhibitors of GLU to therapy acute drug-inducing enteropathy in clinic.
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Affiliation(s)
- Lei Feng
- College of Integrative Medicine, College of Pharmacy, the National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, Dalian Medical University, Dalian 116044, China
- Center for Molecular Medicine, School of Life Science and Biotechnology, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Yongliang Yang
- Center for Molecular Medicine, School of Life Science and Biotechnology, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Xiaokui Huo
- College of Integrative Medicine, College of Pharmacy, the National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, Dalian Medical University, Dalian 116044, China
| | - Xiangge Tian
- College of Integrative Medicine, College of Pharmacy, the National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, Dalian Medical University, Dalian 116044, China
| | - Yujie Feng
- College of Integrative Medicine, College of Pharmacy, the National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, Dalian Medical University, Dalian 116044, China
| | - Hanwen Yuan
- TCM and Ethnomedicine Innovation & Development International Laboratory, Sino-Pakistan TCM and Ethnomedicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Lijian Zhao
- Bio/Medical Experiment Center, College of Biology, Hunan University, Changsha 410082, China
| | - Chao Wang
- College of Integrative Medicine, College of Pharmacy, the National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, Dalian Medical University, Dalian 116044, China
- Center for Molecular Medicine, School of Life Science and Biotechnology, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Peng Chu
- Center for Molecular Medicine, School of Life Science and Biotechnology, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Feida Long
- Center for Molecular Medicine, School of Life Science and Biotechnology, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Wei Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, Sino-Pakistan TCM and Ethnomedicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Xiaochi Ma
- College of Integrative Medicine, College of Pharmacy, the National & Local Joint Engineering Research Center for Drug Development of Neurodegenerative Disease, Dalian Medical University, Dalian 116044, China
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Ali S, Khan FI, Chen W, Rahaman A, Wang Y. Open and closed states of Mrlip1 DAG lipase revealed by molecular dynamics simulation. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1513647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Shahid Ali
- School of Food Science and Engineering, South China University of Technology, Guangzhou, People’s Republic of China
| | - Faez Iqbal Khan
- Department of Chemistry, Rhodes University, Grahamstown, South Africa
| | - Wenwen Chen
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Abdul Rahaman
- School of Food Science and Engineering, South China University of Technology, Guangzhou, People’s Republic of China
| | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, People’s Republic of China
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43
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Elucidation of interaction mechanism of ellagic acid to the integrin linked kinase. Int J Biol Macromol 2018; 122:1297-1304. [PMID: 30227205 DOI: 10.1016/j.ijbiomac.2018.09.089] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 12/20/2022]
Abstract
Integrin-linked kinase (ILK) is a member of Ser/Thr kinase which interacts to the cytoplasmic domain of β-integrins, and thereby induces apoptosis. ILK is considered as potential drug target because it's direct involvement in the tumor progression. Here, we have performed molecular docking followed by 100 ns MD simulation to understand the mechanism of interaction of ILK with the ellagic acid (EA). EA is well known for its antiproliferative and antioxidant properties in cancer cell lines and animal models. We have observed that EA binds to the active site cavity of ILK and causes conformational changes in the ILK structure. The orientation of EA in the active pocket of ILK showed to have least RMSD values and stable. The average binding energy ILK-EA complex calculated during MMPBSA was -191.267 kJ/mol, indicating a relatively strong binding affinity. The actual binding affinity of EA to ILK was measured by fluorescence spectroscopy and Kb and n values were 9.28 μM and 1.9264 (~2), respectively. The IC50 values for EA were 26.22 ± 0.12 μM for MCF-7 and 38.45 ± 2.42 μM for HepG2 cells, estimated by MTT assay. Our findings are helpful to design EA-based novel inhibitors of ILK which have potential to attenuate tumor progression.
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44
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Stapleton M, Arunkumar N, Kubaski F, Mason RW, Tadao O, Tomatsu S. Clinical presentation and diagnosis of mucopolysaccharidoses. Mol Genet Metab 2018; 125:4-17. [PMID: 30057281 DOI: 10.1016/j.ymgme.2018.01.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 01/04/2018] [Indexed: 01/09/2023]
Abstract
Mucopolysaccharidoses (MPS) are estimated to affect1 in 25,000 live births although specific rates vary between the ethnic origin and country. MPS are a group of lysosomal storage disorders, which cause the buildup of GAG(s) due to insufficient or absent GAG-degrading enzymes. With seven types of MPS disorders and eleven subtypes, the MPS family presents unique challenges for early clinical diagnosis due to the molecular and clinical heterogeneity between groups and patients. Novel methods of early identification, particularly newborn screening through mass spectrometry, can change the flow of diagnosis, allowing enzyme and GAG quantification before the presentation of clinical symptoms improving outcomes. Genetic testing of patients and their families can also be conducted preemptively. This testing enables families to make informed decisions about family planning, leading to prenatal diagnosis. In this review, we discuss the clinical symptoms of each MPS type as they initially appear in patients, biochemical and molecular diagnostic methods, and the future of newborn screening for this group of disorders.
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Affiliation(s)
- Molly Stapleton
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States; Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Nivethitha Arunkumar
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States; Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Francyne Kubaski
- Department of Molecular Biology and Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Robert W Mason
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States; Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Orii Tadao
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Shunji Tomatsu
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States; Department of Biological Sciences, University of Delaware, Newark, DE, United States; Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan; Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA, United States; Department of Pediatrics, Shimane University, Shimane, Japan.
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45
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Mohammad T, Khan FI, Lobb KA, Islam A, Ahmad F, Hassan MI. Identification and evaluation of bioactive natural products as potential inhibitors of human microtubule affinity-regulating kinase 4 (MARK4). J Biomol Struct Dyn 2018; 37:1813-1829. [PMID: 29683402 DOI: 10.1080/07391102.2018.1468282] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Microtubule affinity-regulating kinase 4 (MARK4) has recently been identified as a potential drug target for several complex diseases including cancer, diabetes and neurodegenerative disorders. Inhibition of MARK4 activity is an appealing therapeutic option to treat such diseases. Here, we have performed structure-based virtual high-throughput screening of 100,000 naturally occurring compounds from ZINC database against MARK4 to find its potential inhibitors. The resulted hits were selected, based on the binding affinities, docking scores and selectivity. Further, binding energy calculation, Lipinski filtration and ADMET prediction were carried out to find safe and better hits against MARK4. Best 10 compounds bearing high specificity and binding efficiency were selected, and their binding pattern to MARK4 was analyzed in detail. Finally, 100 ns molecular dynamics simulation was performed to evaluate; the dynamics stability of MARK4-compound complex. In conclusion, these selected natural compounds from ZINC database might be potential leads against MARK4, and can further be exploited in drug design and development for associated diseases.
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Affiliation(s)
- Taj Mohammad
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi , 110025 , India
| | - Faez Iqbal Khan
- b Computational Mechanistic Chemistry and Drug Discovery , Rhodes University , Grahamstown , South Africa
| | - Kevin A Lobb
- b Computational Mechanistic Chemistry and Drug Discovery , Rhodes University , Grahamstown , South Africa
| | - Asimul Islam
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi , 110025 , India
| | - Faizan Ahmad
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi , 110025 , India
| | - Md Imtaiyaz Hassan
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi , 110025 , India
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46
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Khan S, Khan FI, Mohammad T, Khan P, Hasan GM, Lobb KA, Islam A, Ahmad F, Imtaiyaz Hassan M. Exploring molecular insights into the interaction mechanism of cholesterol derivatives with the Mce4A: A combined spectroscopic and molecular dynamic simulation studies. Int J Biol Macromol 2018; 111:548-560. [DOI: 10.1016/j.ijbiomac.2017.12.160] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/16/2017] [Accepted: 12/30/2017] [Indexed: 01/08/2023]
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47
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Syed SB, Shahbaaz M, Khan SH, Srivastava S, Islam A, Ahmad F, Hassan MI. Estimation of pH effect on the structure and stability of kinase domain of human integrin-linked kinase. J Biomol Struct Dyn 2018; 37:156-165. [DOI: 10.1080/07391102.2017.1420492] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sunayana Begum Syed
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Mohd Shahbaaz
- South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
| | - Sabab Hassan Khan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Saurabha Srivastava
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Asimul Islam
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Faizan Ahmad
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Md. Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
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48
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Queen A, Khan P, Idrees D, Azam A, Hassan MI. Biological evaluation of p-toluene sulphonylhydrazone as carbonic anhydrase IX inhibitors: An approach to fight hypoxia-induced tumors. Int J Biol Macromol 2018; 106:840-850. [DOI: 10.1016/j.ijbiomac.2017.08.082] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/10/2017] [Accepted: 08/13/2017] [Indexed: 10/19/2022]
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49
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Cheng KW, Tseng CH, Yang CN, Tzeng CC, Cheng TC, Leu YL, Chuang YC, Wang JY, Lu YC, Chen YL, Cheng TL. Specific Inhibition of Bacterial β-Glucuronidase by Pyrazolo[4,3-c]quinoline Derivatives via a pH-Dependent Manner To Suppress Chemotherapy-Induced Intestinal Toxicity. J Med Chem 2017; 60:9222-9238. [DOI: 10.1021/acs.jmedchem.7b00963] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Kai-Wen Cheng
- Institute of Biomedical
Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Chih-Hua Tseng
- School of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Fragrance
and Cosmetic Science, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Research
Center for Natural Products and Drug Development, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chia-Ning Yang
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan
| | - Cherng-Chyi Tzeng
- Research
Center for Natural Products and Drug Development, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department
of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Ta-Chun Cheng
- Center
for Biomarkers and Biotech Drugs, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yu-Lin Leu
- Department
of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan City 717, Tainan
| | - Yu-Chung Chuang
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan
| | - Jaw-Yuan Wang
- Graduate Institute
of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Division of Gastroenterology and General Surgery, Department
of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yun-Chi Lu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yeh-Long Chen
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department
of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Tian-Lu Cheng
- Institute of Biomedical
Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- Center
for Biomarkers and Biotech Drugs, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Biomedical and Environmental
Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
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Naz F, Khan FI, Mohammad T, Khan P, Manzoor S, Hasan GM, Lobb KA, Luqman S, Islam A, Ahmad F, Hassan MI. Investigation of molecular mechanism of recognition between citral and MARK4: A newer therapeutic approach to attenuate cancer cell progression. Int J Biol Macromol 2017; 107:2580-2589. [PMID: 29079437 DOI: 10.1016/j.ijbiomac.2017.10.143] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 10/22/2017] [Accepted: 10/23/2017] [Indexed: 10/18/2022]
Abstract
Microtubule affinity regulating kinase 4 (MARK4) is a member of AMP-activated protein kinase, found to be involved in apoptosis, inflammation and many other regulatory pathways. Since, its aberrant expression is directly associated with the cell cycle and thus cancer. Therefore, MARK4 is being considered as a potential drug target for cancer therapy. Here, we investigated the mechanism of inhibition of MARK4 activity by citral. Docking studies suggested that citral effectively binds to the active site cavity, and complex is stabilized by several interactions. We further performed molecular dynamics simulation of MARK4-citral complex under explicit water condition for 100ns and observed that binding of citral to MARK4 was quite stable. Fluorescence binding studies suggested that citral strongly binds to MARK4 and thereby inhibits its enzyme activity which was measured by the kinase inhibition assay. We further performed MTT assay and observed that citral inhibits proliferation of breast cancer cell line MCF-7. This work provides a newer insight into the use of citral as novel cancer therapeutics through the MARK4 inhibition. Results may be employed to design novel therapeutic molecule using citral as a scaffold for MARK4 inhibition to fight related diseases.
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Affiliation(s)
- Farha Naz
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India; Department of Molecular & Cellular Engineering, Sam Higginbottom Institute of Agriculture, Technology and Sciences, Allahabad, 211 007, Uttar Pradesh, India
| | - Faez Iqbal Khan
- Department of Chemistry, Rhodes University, Grahamstown 6139, South Africa
| | - Taj Mohammad
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Parvez Khan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Saaliqa Manzoor
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Kevin A Lobb
- Department of Chemistry, Rhodes University, Grahamstown 6139, South Africa
| | - Suaib Luqman
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Asimul Islam
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Faizan Ahmad
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Md Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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